Collagen-induced arthritis (CIA) and pristane-induced arthritis (PIA) in rats are well-established experimental animal models that have been used to gain insight into the pathogenesis of rheumatoid arthritis (RA), a chronic and commonly disabling disease with a prevalence of 1% in most populations. CIA, PIA and RA are complex trait diseases regulated by MHC and non-MHC genes. Non-MHC genes account for 50-75% of the genetic contribution to RA, yet, little is known about those genes. The underlying hypotheses of this proposal are that the non-MHC loci governing susceptibility to and severity of CIA and PIA in rats will be highly relevant to understanding the pathogenesis of RA and could generate new targets for the development of more specific therapies, as well as new biomarkers for diagnosis and prognosis. In experiments leading up to the present proposal, a genome-wide screen done in an F2 intercross between the MHC identical arthritis- susceptible DA and the arthritis-resistant ACI inbred rat strains studied for CIA identified three non-MHC quantitative trait loci (QTL) Cia7, C/a70and C/a27on chromosomes 2, 2, and 10, respectively. Genotype- guided QTL-congenic strains were generated. DA.ACI(CialO) rats developed a significantly milder form of arthritis, typically with no synovial hyperplasia or pannus formation, and preservation of the joint architecture, compared with DA. The transfer of the Cia27 interval from DA into ACI.DA(Cia27) congenics, was enough to render these rats susceptible to CIA. Thus, it is hypothesized that the robust and highly penetrant phenotype of CIA and PIA depends on the presence of susceptibility alleles at Cia7, C/a70and Cia27. Additionally, Cia7, C/a70and C/a27are located in regions syntenic to those containing loci regulating different forms of autoimmune diseases, including RA, suggesting that these rat genes will be relevant to human disease. This proposal aims at identifying and characterizing those genes. In Aim 1 the critical regions containing the arthritis genes will be progressively reduced to <1 Mb in recombinant subcongenics. Sub-phenotypes relevant to arthritis will continue to be identified and will be studied in congenics to obtain early clues to gene function and identity. In Aim 2 candidate genes within the critical regions of C/a70and C/a27will be sequenced and analyzed for disease-causing polymorphisms/mutations that differentiate DA from ACI. The identified genes and alleles will be functionally characterized in in vitro and in vivo studies.